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PubMed2006

Real-life applications of the MULVADO software package for processing DOSY NMR data.

MULVADO is a newly developed software package for DOSY NMR data processing, based on multivariate curve resolution (MCR), one of the principal multivariate methods for processing DOSY data. This paper will evaluate this software package by using real-life data of materials used in the printing industry: two data sets from the same ink sample but of different quality. Also a sample of an organic photoconductor and a toner sample are analysed. Compared with the routine DOSY output from monoexponential fitting, one of the single channel algorithms in the commercial Bruker software, MULVADO provides several advantages. The key advantage of MCR is that it overcomes the fluctuation problem (non-consistent diffusion coefficient of the same component). The combination of non-linear regression (NLR) and MCR can yield more accurate resolution of a complex mixture. In addition, the data pre-processing techniques in MULVADO minimise the negative effects of experimental artefacts on the results of the data. In this paper, the challenges for analysing polymer samples and other more complex samples will also be discussed.

Magnetic Resonance Spectroscopy↗

PubMed2003

PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry.

A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimental MS/MS data. These methods suffer from several drawbacks and cannot be used for the identification of proteins from unknown genomes. In this communication, we describe a new de novo sequencing software package, PEAKS, to extract amino acid sequence information without the use of databases. PEAKS uses a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum. The output of the software gives amino acid sequences with confidence scores for the entire sequences, as well as an additional novel positional scoring scheme for portions of the sequences. The performance of PEAKS is compared with Lutefisk, a well-known de novo sequencing software, using quadrupole-time-of-flight (Q-TOF) data obtained for several tryptic peptides from standard proteins.

Amino Acid Sequence↗

PubMed1993

Interfacing U.S. census map files with statistical graphics software: application and use in epidemiology.

In 1990, the United States Bureau of the Census released detailed geographic map files known as TIGER/Line (Topologically Integrated Geographic Encoding and Referencing). The TIGER files, accessible through purchase or federal repository libraries, contain 24 billion characters of data describing various geographic features including coastlines, hydrography, transportation networks, political boundaries, etc. for the entire United States. Many of these physical features are of potential interest in epidemiological case studies. Unfortunately, the TIGER data base only provides raw alphanumeric data; no utility software, graphical or otherwise, is included. Recently, the S statistical software package has been extended to include a map display function. The map function augments S's high-level approach towards statistical analysis and graphical display of data. Coupling this statistical software with the map data base developed for U.S. Census data collection will facilitate epidemiological research. We discuss the technical background necessary to utilize the TIGER data base for mapping with S. Two types of S maps, segment-based and polygon-based, are discussed along with methods to construct them from TIGER data. Polygon-based maps are useful for displaying regional statistical data, such as disease rates or incidence at the census tract level. Segment-based maps are easier to assemble and are appropriate when the data are not regionalized. Census tract data of AIDS incidence in San Francisco and lung cancer case locations relative to petrochemical refinery sites in Contra Costa County are used to illustrate the methods and potential uses of interfacing the TIGER data base with S.

Acquired Immunodeficiency Syndrome↗

PubMed1998

Improved hardware and software for single-crystal NMR spectroscopy.

Design of state-of-the-art instrumentation and software for acquisition and analysis of single-crystal NMR spectra is presented. The design involves highly accurate rotation of a goniometer, and the acquisition of all the spectra for each rotation axis is automatically controlled by the host computer of the spectrometer using a homebuilt interface between the computer and the single-crystal probe. Moreover, a software package (ASICS) for fast and routine assignment/analysis of complex single-crystal spectra has been developed. Employing this equipment, the acquisition and complete analysis of single-crystal NMR spectra may be performed in about the same time as required for powder methods (spinning or static). The hardware and software are compared to recent alternative approaches within single-crystal NMR. Finally, it has been observed that single-crystal NMR techniques may provide the desired data for samples where powder methods fail.

Computers↗

PubMedDate not supplied

IVE (Image Visualization Environment): a software platform for all three-dimensional microscopy applications.

IVE (Image Visualization Environment) is a software platform designed from the outset to handle all aspects of modern computerized multidimensional microscopy. This platform provides users with an execution environment in which 5D data (XYZ, wavelength, and time) can be easily manipulated for the purpose of data collection, processing, display, and analysis. During the entire process, powerful data display functions are readily available for extracting complicated three-dimensional information through data visualization. By employing both the shared memory and multitasking features of the UNIX operation system, individual functions can be implemented as separate programs, and multiple programs can access the same data pool simultaneously. This enables users to combine the functionalities of different programs to facilitate each unique data analysis task. Furthermore, by defining an appropriate program execution model, commonly shared functional components such as data display, data I/O and user interface, etc. can be implemented using simple IVE library calls. This dramatically reduces the program development time and ensures consistency throughout the entire software system. As a result, users can quickly master the microscopy software system and new functions can be easily integrated, as different functional requirements arise for different research projects.

Chromosomes↗

PubMed1998

QVIEW: software for rapid selection of particles from digital electron micrographs.

The QVIEW image-processing software package provides a graphical user interface for interactive and rapid selection of particles from digital electron micrographs. This package was developed to facilitate the selection of elliptical, hydrophobic, and aggregating particles, which present complications for other particle selection packages. Speed improvements have been attained by using the fast graphics routines available in the Tc1/Tk toolkit and by separating the time consuming image-processing procedures from the interactive selection steps. The software is based on C++ and Tc1/Tk, both of which are readily available on many computer platforms. Processing features include removal of oversaturated pixels, planar subtraction using three or more background regions, exclusion of unwanted density such as nearby particles, and application of a circular or elliptical mask. Particles, along with their corresponding background and exclude regions, may be selected interactively from multiple digital micrographs, and the selection parameters are saved in a disk file for later processing. C shell processing scripts are easily modified and customized for specific applications. In summary, this software package enables the user-friendly, rapid selection of particles suitable for input into three-dimensional reconstruction packages.

Computers↗

PubMed2006

Use of ICM+ software for on-line analysis of intracranial and arterial pressures in head-injured patients.

OBJECTIVE: To summarize our experience from the first 2 years of use of the ICM+ software in our Neurocritical Care Unit (NCCU). MATERIALS AND METHODS: Ninety-five head-injured patients (74 males, 21 females), average age 36 years, were managed in the NCCU. Intracranial pressure (ICP) was monitored using Codman intraparenchymal probes and arterial blood pressure (ABP) was measured from the radial artery. Signals were monitored by ICM+ software calculating mean values of ICP, ABP, cerebral perfusion pressure (CPP) and various indices describing pressure reactivity, compensation and vascular waveforms of ICP (pulse amplitude, respiratory, and slow waves), etc. RESULTS: Mean ICP was 17 mmHg, mean CPP was 73 mmHg. Seven patients showed permanent disturbance of cerebral autoregulation (mean pressure reactivity index above 0.3). Pressure reactivity index demonstrated significant U-shape relationship with CPP, suggesting loss of pressure reactivity at too low (CPP < 55 mmHg) and too high CPPs (CPP > 95 mmHg). Mean ICP was inversely correlated with respiratory rate (R = 0.46; p < 0.0001; reciprocal model). CONCLUSION: The new version of ICM+ software proved to be useful clinically in the NCCU. It allows continuous monitoring of pressure reactivity and exploratory analysis of factors implicating intracranial hypertension.

Adult↗

PubMed2005

ICM+: software for on-line analysis of bedside monitoring data after severe head trauma.

ICM software was developed in 1986 in Warsaw, Poland and has been in use at the University of Cambridge Neurocritical Care Unit for 10 years collecting data from bed-side monitors in nearly 600 severely head injured patients and calculating secondary indices describing cerebral autoregulation and pressure-volume compensation. The new software ICM+ includes a much extended calculation engine that allows easy configuration and on-line trending of complex parameters. The program records raw signals, and calculates time trends of summary parameters. Configuration and analysis utilises arithmetic expressions of signal processing functions to calculate various statistical properties for each signal, frequency spectrums and derivatives, as well as correlations/cross-correlations between signals. The software allows configuration of several levels of analysis before calculating the final time trends. The final data are displayed in a variety of ways including simple time trends, as well as time window based histograms, cross histograms, correlations etc. All this allows complex information coming off the bed-side monitors to be summarized in a concise fashion and presented to medical and nursing staff in a simple way that alerts them to the development of various pathological processes. The system provides a universal tool for clinical and academic purposes. Its flexibility and advanced signal processing is specialized for the needs of multidisciplinary brain monitoring.

Craniocerebral Trauma↗

PubMed1988

The design and implementation of a software system for clinical studies: an illustration based on the needs of a comprehensive cancer center.

A computerized system for the management of a clinical research database has been developed with several attractive features. This relational database management system allows for screen-driven data entry, data checking, system security, and report generation in a timely manner. In addition, the system is cost-effective in a number of ways: (1) development time is considerably reduced due to the inherent programming features of the software, (2) once developed the system can be maintained by nontechnical personnel thereby reducing personnel costs, (3) the system can be developed and maintained on a microcomputer system, and (4) the commercial software used in our system is periodically updated thereby assuring the user of state-of-the-art technology. Beyond the initial expenditures for hardware and software, no additional system costs are incurred. While this system, currently adopted by the Yale Comprehensive Cancer Center, represents an effective approach to handling the data-management needs of a large, single-institution cancer research center, the design and programming methodology can be readily adapted to other research settings.

Cancer Care Facilities↗

PubMed1989

Fitting heteroscedastic regression models to individual pharmacokinetic data using standard statistical software.

In the analysis of individual pharmacokinetic data by nonlinear regression it is important to allow for possible heterogeneity of variance in the response. Two common methods of doing this are weighted least squares with appropriate weights or data transformation using a suitable transform. With either approach it is appealing to let the data determine the appropriate choice of weighting scheme or transformation. This article describes two methods of doing this which are easy to compute using standard statistical software. The first method is a generalized least squares scheme for the case where the variance is assumed proportional to an unknown power of the mean. The second involves applying a power transformation to both sides of the regression equation. It is shown that both techniques may be implemented using only nonlinear regression routines. Sample code is provided for their implementation using the SAS software package. However, the proposed methods are feasible using any software package that incorporates a nonlinear least squares routine, and are thus well suited to routine use.

Humans↗

PubMed1991

CINA: a software to Compose INfusion sheets for i.v. Anesthetic drugs.

CINA is a software which uses LOTUS 1-2-3 commands and macros and it runs on an IBM PC. It contains an extensive database of three sections. Section 1 includes a list of several models of commercialized infusion devices. Section 2 presents the available IV packagings for a list of IV drugs. Section 3 contains the record of IV standard infusion regimens for each drug. Any other new infusion device, drug, or standard infusion regimen can be added or modified. The software verifies the compatibility of the prescribed infusion device according to the available drug packaging contained in the database. Moreover, it converts the infusion steps into the flow-rate units of the selected infusion device according to the patient's weight and the chosen drug concentration. Finally, the software allows the storage of all the information on a disk file or outputting on a printer.

Anesthesia, Intravenous↗

PubMed1996

A comparison of a Bayesian population method with two methods as implemented in commercially available software.

In this paper we describe and discuss three specific estimation procedures that are available within commercially available population software packages. The first version of NONMEM (l) was released in 1979 and later versions are the standard analysis tools in both industry and academia. Recently, two commercially available pieces of software have become available. PPHARM was released during 1994 and POPKAN was released in 1995. We provide descriptions and critique the FOCE method within NONMEM, the two-step algorithm within PPHARM and the Markov chain Monte Carlo method that is utilized by POPKAN. We use simulated data generated from a monoexponential model to evaluate the parameter estimation capabilities of these methods within the three software tools. In particular we investigate the effect on parameter estimation of increasing both interindividual and intraindividual variability.

Bayes Theorem↗

PubMed2003

Improved accuracy in estimation of left ventricular function parameters from QGS software with Tc-99m tetrofosmin gated-SPECT: a multivariate analysis.

UNLABELLED: The purpose of this study was to verify whether the accuracy of left ventricular parameters related to left ventricular function from gated-SPECT improved or not, using multivariate analysis. METHODS: Ninety-six patients with cardiovascular diseases were studied. Gated-SPECT with the QGS software and left ventriculography (LVG) were performed to obtain left ventricular ejection fraction (LVEF), end-diastolic volume (EDV) and end-systolic volume (ESV). Then, multivariate analyses were performed to determine empirical formulas for predicting these parameters. The calculated values of left ventricular parameters were compared with those obtained directly from the QGS software and LVG. RESULTS: Multivariate analyses were able to improve accuracy in estimation of LVEF, EDV and ESV. Statistically significant improvement was seen in LVEF (from r = 0.6965 to r = 0.8093, p < 0.05). Although not statistically significant, improvements in correlation coefficients were seen in EDV (from r = 0.7199 to r = 0.7595, p = 0.2750) and ESV (from r = 0.5694 to r = 0.5871, p = 0.4281). CONCLUSION: The empirical equations with multivariate analysis improved the accuracy in estimating LVEF from gated-SPECT with the QGS software.

Adolescent↗

PubMed2001

Integrating digital educational content created and stored within disparate software environments: an extensible markup language (XML) solution in real-world use.

OBJECTIVE: To provide a standardized and scaleable mechanism for exchanging digital radiologic educational content between software systems that use disparate authoring, storage, and presentation technologies. MATERIALS/METHODS: Our institution uses two distinct software systems for creating educational content for radiology. Each system is used to create in-house educational content as well as commercial educational products. One system is an authoring and viewing application that facilitates the input and storage of hierarchical knowledge and associated imagery, and is capable of supporting a variety of entity relationships. This system is primarily used for the production and subsequent viewing of educational CD-ROMS. Another software system is primarily used for radiologic education on the world wide web. This system facilitates input and storage of interactive knowledge and associated imagery, delivering this content over the internet in a Socratic manner simulating in-person interaction with an expert. A subset of knowledge entities common to both systems was derived. An additional subset of knowledge entities that could be bidirectionally mapped via algorithmic transforms was also derived. An extensible markup language (XML) object model and associated lexicon were then created to represent these knowledge entities and their interactive behaviors. Forward-looking attention was exercised in the creation of the object model in order to facilitate straightforward future integration of other sources of educational content. XML generators and interpreters were written for both systems. RESULTS: Deriving the XML object model and lexicon was the most critical and time-consuming aspect of the project. The coding of the XML generators and interpreters required only a few hours for each environment. Subsequently, the transfer of hundreds of educational cases and thematic presentations between the systems can now be accomplished in a matter of minutes. The use of algorithmic transforms results in nearly 100% transfer of context as well as content, thus providing "presentation-ready" outcomes. CONCLUSION: The automation of knowledge exchange between dissimilar digital teaching environments magnifies the efforts of educators and enriches the learning experience for participants. XML is a powerful and useful mechanism for transfering educational content, as well as the context and interactive behaviors of such content, between disparate systems.

Computer Storage Devices↗

PubMed2001

Creation of a software application for the clinical radiologist.

PURPOSE: To create a software application that automates a significant portion of a clinical radiologist's work. METHODS: The daily workflow of clinical radiologists in a university-based department was analyzed, specifically looking for manual tasks that could be implemented in software. An application that a practicing radiologist would use in his daily work was created. RESULTS: By using speech recognition, reports could be created, edited, and verified immediately. Online medical reference information could be made instantly accessible. Billing data could be captured accurately and completely at report creation time. A radiologist could be alerted to important upcoming events by use of a reminder system. Reports could be delivered immediately to referring physicians using either the internet or telephone. CONCLUSIONS: It is possible to improve the productivity of busy practicing clinical radiologists by automating a large portion of their workflow and implementing it in an easily mastered software application.

Humans↗

PubMed2001

[Computer-assisted surgical planning. 3-D software for the PC].

A potent software was developed for virtual planning in orthopedic surgery with complex spatial relationships, that runs on a standard PC with Windows 98/NT/2000. This voxel-based 3D-software creates data from tomographic images (CT, MRI, 3D-Sono, PET) in Dicom-III-format, that are visualized in near real-time as 2D-reconstructions or 3D-images. For three-dimensional analysis interactive tools, geometric rulers and an anatomic coordinate-system are available. Multiplanar osteotomies are carried out with a virtual saw. Selected segments are moved freely to mimic fracture reduction and deformity correction. Three-dimensional movement coordination is supported by problem-oriented movement features and a 3D-mouse. User defined objects in CAD-format like implants or anatomical templates can be inserted and moved. Matching of two volume data sets is possible as well as simultaneous processing of different data sets. All 3D-reconstructions can be calculated as virtual radiographs and viewed stereoscopically with LCD-shutter glasses. Export features in various data formats allow further processing of all volume data in CAD applications and rapid prototyping. An intra-operative navigation system can be integrated via an interface. This universally applicable software allows thorough three-dimensional analysis and processing of volume data sets from tomographic images and can be used in various applications through its flexible modular setup.

Diagnostic Imaging↗

PubMed2001

Validation of a software designed for computed tomographic (CT) measurement of lung water.

OBJECTIVE: The in-vitro validation of a computed tomographic (CT) software specifically designed for quantifying the volume of water contained in the lung. DESIGN: An in-vitro, ex-vivo study. In 1993, a postmortem left pneumonectomy was performed in a patient who died from acute respiratory distress syndrome. The lung was fixed, inflated and dried according to a technique proposed by Markarian and Dailey in 1975 aimed at producing a lung specimen spongy in texture and suitable for radiography. MEASUREMENTS AND RESULTS: In 1999, 13 CT scans of this lung specimen were performed corresponding to different bronchial instillations of known volumes of water and albumin 4%. The different lung weights resulting from the successive bronchial instillations were calculated using a specially designed software, Lungview, adapted for CT measurements and compared with the actual lung weight measured by an electronic scale. The increase in lung weight measured by Lungview was closely correlated with the actual increase in lung weight resulting from bronchial instillation of water and albumin (y = 0.99x - 23, r = 1 for water and y = x - 17, r = 1 for albumin 4%) and the precision of the bias was 7 g for water and 3 g for albumin 4%. CONCLUSIONS: This study shows that the CT software Lungview accurately measured the volume of lung water present within an air-dried exsanguine human lung.

Aged↗

PubMed2003

PF-IND: probability algorithm and software for separation of plant and fungal sequences.

The separation of plant and fungal sequences in EST pools by bioinformatic methods is difficult because of sequence similarities between plants and fungi, lack of enough sequence information, and the short length of the isolated fragments. An algorithm and software that utilize the differences in codon usage bias to discriminate between plant and fungal sequences are described. The software (PF-IND) includes five pairs of fungi and their host plants that can be used to analyze a large number of related species. Analysis of a sequence provides an arbitrary value that defines the likelihood that a sequence will be a fungal or a plant gene. The software can distinguish between homologous fungal and plant genes and it helps identify the correct reading frame of unknown expressed sequence tags (ESTs) for which BLAST analyses do not provide clear information. Short sequences of 100-150 bp can be analyzed with high confidence. PF-IND analysis of 100 sequences derived from fungal infected plants identified the origin of 94 sequences. Only 66 sequences were identified by a BLASTX analysis of the same 100 ESTs. Overall, PF-IND is a novel bioinformatic tool aimed at assisting the research of fungus-plant interactions.

Algorithms↗